As of coming 10 th of April, Google search console will link data to Google selected canonical URLs, not URL referred to by Google search. Why ? Google want to eliminate the duplicate links which happens when you use tools like AMP. Search console metrics will choose Google preferred canonical as the base URL for canonical listing eliminating the confusion created by duplicate links for mobile and PC.
This is going to affect your SEO because your traffic may move away from the link through which it is currently fetched. If you are lucky, your new canonical URL will make up for the lost traffic. If not, you might be seeing a dip in traffic if you are using duplicate URLs and Google chose a different URL as canonical.
You can use the URL inspection tool within the search console before it is too late to determine the canonical URL of a particular URL.